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Advancing Precision Vaccinology by Molecular and Genomic Surveillance of Severe Acute Respiratory Syndrome Coronavirus 2 in Germany, 2021.
Oh, Djin Ye; Hölzer, Martin; Paraskevopoulou, Sofia; Trofimova, Maria; Hartkopf, Felix; Budt, Matthias; Wedde, Marianne; Richard, Hugues; Haldemann, Berit; Domaszewska, Teresa; Reiche, Janine; Keeren, Kathrin; Radonic, Aleksandar; Ramos Calderón, Julia Patricia; Smith, Maureen Rebecca; Brinkmann, Annika; Trappe, Kathrin; Drechsel, Oliver; Klaper, Kathleen; Hein, Sascha; Hildt, Eberhardt; Haas, Walter; Calvignac-Spencer, Sébastien; Semmler, Torsten; Dürrwald, Ralf; Thürmer, Andrea; Drosten, Christian; Fuchs, Stephan; Kröger, Stefan; von Kleist, Max; Wolff, Thorsten.
  • Oh DY; Influenza and Other Respiratory Viruses (FG17), Robert Koch Institute, Berlin, Germany.
  • Hölzer M; Methodology and Research Infrastructure, Bioinformatics and Systems Biology (MF1), Robert Koch Institute, Berlin, Germany.
  • Paraskevopoulou S; Methodology and Research Infrastructure, Bioinformatics and Systems Biology (MF1), Robert Koch Institute, Berlin, Germany.
  • Trofimova M; Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany.
  • Hartkopf F; Methodology and Research Infrastructure, Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany.
  • Budt M; Influenza and Other Respiratory Viruses (FG17), Robert Koch Institute, Berlin, Germany.
  • Wedde M; Influenza and Other Respiratory Viruses (FG17), Robert Koch Institute, Berlin, Germany.
  • Richard H; Methodology and Research Infrastructure, Bioinformatics and Systems Biology (MF1), Robert Koch Institute, Berlin, Germany.
  • Haldemann B; Methodology and Research Infrastructure, Bioinformatics and Systems Biology (MF1), Robert Koch Institute, Berlin, Germany.
  • Domaszewska T; Respiratory Infections (FG36), Robert Koch Institute, Berlin, Germany.
  • Reiche J; Influenza and Other Respiratory Viruses (FG17), Robert Koch Institute, Berlin, Germany.
  • Keeren K; Gastroenteritis and Hepatitis Pathogens and Enteroviruses (FG15), Robert Koch Institute, Berlin, Germany.
  • Radonic A; Methodology and Research Infrastructure, Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany.
  • Ramos Calderón JP; Influenza and Other Respiratory Viruses (FG17), Robert Koch Institute, Berlin, Germany.
  • Smith MR; Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany.
  • Brinkmann A; Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS1), Robert Koch Institute, Berlin, Germany.
  • Trappe K; Methodology and Research Infrastructure, Bioinformatics and Systems Biology (MF1), Robert Koch Institute, Berlin, Germany.
  • Drechsel O; Methodology and Research Infrastructure, Bioinformatics and Systems Biology (MF1), Robert Koch Institute, Berlin, Germany.
  • Klaper K; Methodology and Research Infrastructure, Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany.
  • Hein S; Sexually Transmitted Bacterial Pathogens and HIV (FG18), Robert Koch Institute, Berlin, Germany.
  • Hildt E; Division of Virology, Paul Ehrlich Institute, Langen, Germany.
  • Haas W; Division of Virology, Paul Ehrlich Institute, Langen, Germany.
  • Calvignac-Spencer S; Gastroenteritis and Hepatitis Pathogens and Enteroviruses (FG15), Robert Koch Institute, Berlin, Germany.
  • Semmler T; Epidemiology of Highly Pathogenic Microorganisms (P3), Viral Evolution, Robert Koch Institute, Berlin, Germany.
  • Dürrwald R; Methodology and Research Infrastructure, Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany.
  • Thürmer A; Influenza and Other Respiratory Viruses (FG17), Robert Koch Institute, Berlin, Germany.
  • Drosten C; Methodology and Research Infrastructure, Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany.
  • Fuchs S; Institute of Virology, Charité-University Medicine Berlin, Berlin, Germany.
  • Kröger S; Methodology and Research Infrastructure, Bioinformatics and Systems Biology (MF1), Robert Koch Institute, Berlin, Germany.
  • von Kleist M; Gastroenteritis and Hepatitis Pathogens and Enteroviruses (FG15), Robert Koch Institute, Berlin, Germany.
  • Wolff T; Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany.
Clin Infect Dis ; 75(Supplement_1): S110-S120, 2022 Aug 15.
Article in English | MEDLINE | ID: covidwho-1992148
ABSTRACT

BACKGROUND:

Comprehensive pathogen genomic surveillance represents a powerful tool to complement and advance precision vaccinology. The emergence of the Alpha variant in December 2020 and the resulting efforts to track the spread of this and other severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern led to an expansion of genomic sequencing activities in Germany.

METHODS:

At Robert Koch Institute (RKI), the German National Institute of Public Health, we established the Integrated Molecular Surveillance for SARS-CoV-2 (IMS-SC2) network to perform SARS-CoV-2 genomic surveillance at the national scale, SARS-CoV-2-positive samples from laboratories distributed across Germany regularly undergo whole-genome sequencing at RKI.

RESULTS:

We report analyses of 3623 SARS-CoV-2 genomes collected between December 2020 and December 2021, of which 3282 were randomly sampled. All variants of concern were identified in the sequenced sample set, at ratios equivalent to those in the 100-fold larger German GISAID sequence dataset from the same time period. Phylogenetic analysis confirmed variant assignments. Multiple mutations of concern emerged during the observation period. To model vaccine effectiveness in vitro, we employed authentic-virus neutralization assays, confirming that both the Beta and Zeta variants are capable of immune evasion. The IMS-SC2 sequence dataset facilitated an estimate of the SARS-CoV-2 incidence based on genetic evolution rates. Together with modeled vaccine efficacies, Delta-specific incidence estimation indicated that the German vaccination campaign contributed substantially to a deceleration of the nascent German Delta wave.

CONCLUSIONS:

SARS-CoV-2 molecular and genomic surveillance may inform public health policies including vaccination strategies and enable a proactive approach to controlling coronavirus disease 2019 spread as the virus evolves.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Experimental Studies / Observational study / Prognostic study / Randomized controlled trials Topics: Vaccines / Variants Limits: Humans Language: English Journal: Clin Infect Dis Journal subject: Communicable Diseases Year: 2022 Document Type: Article Affiliation country: Cid

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Experimental Studies / Observational study / Prognostic study / Randomized controlled trials Topics: Vaccines / Variants Limits: Humans Language: English Journal: Clin Infect Dis Journal subject: Communicable Diseases Year: 2022 Document Type: Article Affiliation country: Cid